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- PDB-7znt: CRYSTAL STRUCTURE OF AT7 IN COMPLEX WITH THE SECOND BROMODOMAIN O... -

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Basic information

Entry
Database: PDB / ID: 7znt
TitleCRYSTAL STRUCTURE OF AT7 IN COMPLEX WITH THE SECOND BROMODOMAIN OF HUMAN BRD4 AND PVHL:ELONGINC:ELONGINB
Components
  • Bromodomain-containing protein 4
  • Elongin-B
  • Elongin-C
  • von Hippel-Lindau disease tumor suppressor
KeywordsLIGASE / PROTAC ternary complex / E3 ligase / PROTAC
Function / homology
Function and homology information


regulation of cellular response to hypoxia / RHOBTB3 ATPase cycle / negative regulation of receptor signaling pathway via JAK-STAT / transcription elongation factor activity / target-directed miRNA degradation / elongin complex / Replication of the SARS-CoV-1 genome / VCB complex / Cul5-RING ubiquitin ligase complex / Cul2-RING ubiquitin ligase complex ...regulation of cellular response to hypoxia / RHOBTB3 ATPase cycle / negative regulation of receptor signaling pathway via JAK-STAT / transcription elongation factor activity / target-directed miRNA degradation / elongin complex / Replication of the SARS-CoV-1 genome / VCB complex / Cul5-RING ubiquitin ligase complex / Cul2-RING ubiquitin ligase complex / intracellular membraneless organelle / SUMOylation of ubiquitinylation proteins / RNA polymerase II C-terminal domain binding / P-TEFb complex binding / negative regulation of DNA damage checkpoint / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / negative regulation of transcription elongation by RNA polymerase II / histone H4 reader activity / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / host-mediated suppression of viral transcription / positive regulation of G2/M transition of mitotic cell cycle / negative regulation of signal transduction / Tat-mediated elongation of the HIV-1 transcript / positive regulation of T-helper 17 cell lineage commitment / Formation of HIV-1 elongation complex containing HIV-1 Tat / ubiquitin-like ligase-substrate adaptor activity / Formation of HIV elongation complex in the absence of HIV Tat / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / : / negative regulation of TORC1 signaling / RNA Polymerase II Pre-transcription Events / RNA polymerase II CTD heptapeptide repeat kinase activity / negative regulation of autophagy / protein serine/threonine kinase binding / transcription corepressor binding / condensed nuclear chromosome / transcription coregulator activity / TP53 Regulates Transcription of DNA Repair Genes / transcription initiation at RNA polymerase II promoter / positive regulation of cell differentiation / transcription elongation by RNA polymerase II / positive regulation of transcription elongation by RNA polymerase II / Vif-mediated degradation of APOBEC3G / Inactivation of CSF3 (G-CSF) signaling / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Evasion by RSV of host interferon responses / Regulation of expression of SLITs and ROBOs / cell morphogenesis / ubiquitin-protein transferase activity / p53 binding / transcription corepressor activity / Antigen processing: Ubiquitination & Proteasome degradation / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / chromosome / Neddylation / microtubule cytoskeleton / regulation of gene expression / regulation of inflammatory response / protein-containing complex assembly / Replication of the SARS-CoV-2 genome / ubiquitin-dependent protein catabolic process / protein-macromolecule adaptor activity / histone binding / cellular response to hypoxia / molecular adaptor activity / DNA-binding transcription factor binding / amyloid fibril formation / Potential therapeutics for SARS / proteasome-mediated ubiquitin-dependent protein catabolic process / transcription coactivator activity / positive regulation of canonical NF-kappaB signal transduction / transcription cis-regulatory region binding / protein stabilization / protein ubiquitination / cilium / chromatin remodeling / negative regulation of cell population proliferation / negative regulation of gene expression / protein serine/threonine kinase activity / DNA damage response / ubiquitin protein ligase binding / chromatin binding / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / chromatin / positive regulation of DNA-templated transcription / enzyme binding / endoplasmic reticulum / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / mitochondrion / proteolysis / nucleoplasm / nucleus / plasma membrane / cytosol
Similarity search - Function
von Hippel-Lindau disease tumour suppressor, beta/alpha domain / von Hippel-Lindau disease tumour suppressor, alpha domain / von Hippel-Lindau disease tumour suppressor, beta domain / VHL superfamily / von Hippel-Lindau disease tumour suppressor, alpha domain superfamily / von Hippel-Lindau disease tumour suppressor, beta domain superfamily / VHL beta domain / VHL box domain / Elongin-C / Elongin B ...von Hippel-Lindau disease tumour suppressor, beta/alpha domain / von Hippel-Lindau disease tumour suppressor, alpha domain / von Hippel-Lindau disease tumour suppressor, beta domain / VHL superfamily / von Hippel-Lindau disease tumour suppressor, alpha domain superfamily / von Hippel-Lindau disease tumour suppressor, beta domain superfamily / VHL beta domain / VHL box domain / Elongin-C / Elongin B / S-phase kinase-associated protein 1-like / SKP1 component, POZ domain / Skp1 family, tetramerisation domain / Found in Skp1 protein family / Bromodomain protein 4, C-terminal / C-terminal domain of bromodomain protein 4 / Brdt, bromodomain, repeat I / Brdt, bromodomain, repeat II / NET domain superfamily / NET domain profile. / : / NET domain / Bromodomain extra-terminal - transcription regulation / SKP1/BTB/POZ domain superfamily / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / bromo domain / Bromodomain / Bromodomain (BrD) profile. / Bromodomain-like superfamily / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Chem-IZR / Bromodomain-containing protein 4 / von Hippel-Lindau disease tumor suppressor / Elongin-C / Elongin-B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsHughes, S.J. / Casement, R. / Ciulli, A.
Funding support1items
OrganizationGrant numberCountry
Other private
Citation
Journal: Nat.Chem.Biol. / Year: 2023
Title: Functional E3 ligase hotspots and resistance mechanisms to small-molecule degraders.
Authors: Hanzl, A. / Casement, R. / Imrichova, H. / Hughes, S.J. / Barone, E. / Testa, A. / Bauer, S. / Wright, J. / Brand, M. / Ciulli, A. / Winter, G.E.
#1: Journal: Biorxiv / Year: 2022
Title: Charting functional E3 ligase hotspots and resistance mechanisms to small-molecule degraders
Authors: Hanzl, A. / Casement, R. / Imrichova, H. / Hughes, S.J. / Barone, E. / Testa, A. / Bauer, S. / Wright, J. / Brand, M. / Ciulli, A. / Winter, G.E.
History
DepositionApr 22, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 14, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 23, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Mar 15, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.3Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Elongin-B
B: Elongin-C
C: von Hippel-Lindau disease tumor suppressor
D: Elongin-B
E: Elongin-C
F: von Hippel-Lindau disease tumor suppressor
G: Bromodomain-containing protein 4
H: Bromodomain-containing protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,00510
Polymers112,9718
Non-polymers2,0332
Water57632
1
A: Elongin-B
B: Elongin-C
C: von Hippel-Lindau disease tumor suppressor
H: Bromodomain-containing protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,5025
Polymers56,4864
Non-polymers1,0171
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Elongin-B
E: Elongin-C
F: von Hippel-Lindau disease tumor suppressor
G: Bromodomain-containing protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,5025
Polymers56,4864
Non-polymers1,0171
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)82.640, 82.640, 169.600
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number145
Space group name H-MP32
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21D
12B
22E
13C
23F
14G
24H

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETGLUGLUAA1 - 981 - 98
21METMETGLUGLUDD1 - 981 - 98
12METMETCYSCYSBB17 - 1122 - 97
22METMETCYSCYSEE17 - 1122 - 97
13PROPROILEILECC61 - 20610 - 155
23PROPROILEILEFF61 - 20610 - 155
14VALVALMETMETGG350 - 45720 - 127
24VALVALMETMETHH350 - 45720 - 127

NCS ensembles :
ID
1
2
3
4

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Components

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Protein , 4 types, 8 molecules ADBECFGH

#1: Protein Elongin-B / EloB / Elongin 18 kDa subunit / RNA polymerase II transcription factor SIII subunit B / SIII p18 / ...EloB / Elongin 18 kDa subunit / RNA polymerase II transcription factor SIII subunit B / SIII p18 / Transcription elongation factor B polypeptide 2


Mass: 11748.406 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ELOB, TCEB2 / Plasmid: PCDFDUET-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q15370
#2: Protein Elongin-C / EloC / Elongin 15 kDa subunit / RNA polymerase II transcription factor SIII subunit C / SIII p15 / ...EloC / Elongin 15 kDa subunit / RNA polymerase II transcription factor SIII subunit C / SIII p15 / Transcription elongation factor B polypeptide 1


Mass: 10974.616 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ELOC, TCEB1 / Plasmid: PCDFDUET-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q15369
#3: Protein von Hippel-Lindau disease tumor suppressor / Protein G7 / pVHL


Mass: 18702.291 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VHL / Plasmid: PCDFDUET-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P40337
#4: Protein Bromodomain-containing protein 4 / Protein HUNK1


Mass: 15060.332 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRD4, HUNK1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O60885

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Non-polymers , 2 types, 34 molecules

#5: Chemical ChemComp-IZR / (2~{S},4~{R})-1-[(2~{R})-3-[6-[2-[(9~{S})-7-(4-chlorophenyl)-4,5,13-trimethyl-3-thia-1,8,11,12-tetrazatricyclo[8.3.0.0^{2,6}]trideca-2(6),4,7,10,12-pentaen-9-yl]ethanoylamino]hexylsulfanyl]-2-[(1-fluoranylcyclopropyl)carbonylamino]-3-methyl-butanoyl]-~{N}-[[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl]-4-oxidanyl-pyrrolidine-2-carboxamide


Mass: 1016.707 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C50H59ClFN9O5S3 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 32 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.96 Å3/Da / Density % sol: 58.44 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 10% (W/V) PEG 8000, 0.1 M TRIS-HCL (PH REMARK 280 7.5) AND 0.1 M MGCL2,

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.975 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 7, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.975 Å / Relative weight: 1
ReflectionResolution: 3→65.94 Å / Num. obs: 25970 / % possible obs: 100 % / Redundancy: 10 % / CC1/2: 0.992 / Rmerge(I) obs: 0.231 / Rpim(I) all: 0.078 / Rrim(I) all: 0.244 / Net I/σ(I): 8.5 / Num. measured all: 258669
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
3-3.1810.20.9664329542340.7130.321.0184100
9-65.949.70.09792919600.9910.0330.10315.399.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
Aimless0.7.7data scaling
PDB_EXTRACT3.27data extraction
MOLREPphasing
xia2data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5T35

5t35


Resolution: 3→65.94 Å / Cor.coef. Fo:Fc: 0.908 / Cor.coef. Fo:Fc free: 0.878 / SU B: 41.577 / SU ML: 0.33 / SU R Cruickshank DPI: 0.3814 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.426 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2547 1420 5.5 %RANDOM
Rwork0.2126 ---
obs0.215 24513 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 161.65 Å2 / Biso mean: 72.28 Å2 / Biso min: 37.56 Å2
Baniso -1Baniso -2Baniso -3
1-0.39 Å20.19 Å20 Å2
2--0.39 Å20 Å2
3----1.25 Å2
Refinement stepCycle: final / Resolution: 3→65.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7163 0 138 32 7333
Biso mean--59.41 51.05 -
Num. residues----887
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0137482
X-RAY DIFFRACTIONr_bond_other_d0.0040.0157112
X-RAY DIFFRACTIONr_angle_refined_deg1.3381.68410143
X-RAY DIFFRACTIONr_angle_other_deg1.1771.60716417
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6195875
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.1721.327407
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.712151287
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9051561
X-RAY DIFFRACTIONr_chiral_restr0.0470.2952
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.028246
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021700
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A27270.05
12D27270.05
21B25430.07
22E25430.07
31C45030.07
32F45030.07
41G34530.07
42H34530.07
LS refinement shellResolution: 3.001→3.078 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.326 96 -
Rwork0.304 1846 -
all-1942 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.7095-0.7112-2.68522.42421.82717.20480.23660.3071-0.0313-0.5305-0.1152-0.7765-0.04380.4851-0.12140.27780.16510.12420.34180.16290.437-27.481635.5528-14.8727
22.13291.1181-0.84126.5353-1.65873.49180.26790.38980.3518-0.616-0.28610.2585-0.5017-0.13810.01820.25580.1470.03360.14260.05340.1883-43.18140.8142-6.8515
31.83841.26560.07736.0275-0.62820.71780.093-0.05150.29460.0103-0.1650.7649-0.1297-0.43320.07190.03630.0995-0.02040.3272-0.1160.1354-54.917321.668511.279
43.678-0.49360.2444.91081.97316.7662-0.0364-0.5210.52520.56230.268-0.6484-0.14590.6669-0.23160.17680.03-0.07440.4549-0.01570.5052-15.8123.377816.4826
56.2408-3.7430.98415.8973-0.24572.68370.116-0.143-0.49610.2163-0.0805-0.04810.44670.1799-0.03550.15980.0848-0.03720.12490.06310.2947-25.5021-9.94227.0326
65.5747-2.14932.46233.4226-0.90422.9930.27740.3577-0.9306-0.2174-0.15840.23980.70930.093-0.11910.28340.07970.0190.1046-0.09870.2174-46.4667-1.7631-10.6753
76.3267-2.21850.55055.8131-0.29653.8331-0.3738-0.41980.57520.31790.18510.1975-0.4632-0.39990.18870.16180.1413-0.0960.1316-0.10150.1326-71.185425.6318-18.4609
84.42251.2221-0.55387.0441-0.16453.6032-0.05380.0037-0.4622-0.1859-0.098-0.11870.482-0.0810.15190.088-0.0551-0.00060.13470.06820.1063-58.8079-15.157319.4387
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 102
2X-RAY DIFFRACTION2B17 - 112
3X-RAY DIFFRACTION3C61 - 301
4X-RAY DIFFRACTION4D1 - 99
5X-RAY DIFFRACTION5E17 - 112
6X-RAY DIFFRACTION6F61 - 301
7X-RAY DIFFRACTION7G350 - 458
8X-RAY DIFFRACTION8H350 - 459

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